diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 9037d7f3c..9f9c33e4f 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -626,6 +626,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     public void initialize() {
         super.initialize();
 
+        if (SCAC.genotypeArgs.samplePloidy != HomoSapiensConstants.DEFAULT_PLOIDY && !doNotRunPhysicalPhasing) {
+            doNotRunPhysicalPhasing = true;
+            logger.info("Currently, physical phasing is not available when ploidy is different than " + HomoSapiensConstants.DEFAULT_PLOIDY + "; therefore it won't be performed");
+        }
+
         if (dontGenotype && emitReferenceConfidence())
             throw new UserException("You cannot request gVCF output and do not genotype at the same time");
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index 7b3c8f182..1587e03c2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -66,12 +66,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "ebf7706007ff609ce34801cb847db46c"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "41892abdb9c04e1a25598f3e72966bfe"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "efe4b4c7ffbdba14ccca2a45a6903ac5"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "a24405faed1002a5cd9e630150044505"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "edf7526c70dcaa6e7c0b914fe9d91ed3"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "c701f8a4f90691ed044243aa851207ac"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ea86317a90452eaf7c075f7a3aae77a"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "abb50a62d1e91812e20eec57cd97c716"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b80866fdd8242a02f1c291caf2e32d92"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "a4a89693cc1b5385b17c805a8b655cc0"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "0435ae2c51aa08c3e2b1c8b9b03e86a4"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "d8f6b1d015ebe6afd1de6dcf1ebb3c63"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -103,12 +103,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "06885cff1d0899f48bee9057eae36eac"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "fa48ebdb25e876431bd79be34502f848"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fd18cafabf0d8fb0ee3118c4cfe1f83b"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "c245b46adb12bcc8491337b84a742b57"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2951d85daebfe5354ba4c20eb99c777f"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8ef4baadf5bc9058377ad8b1f8d69701"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "efe4e8e4d28d419e40945a948fd5bdd0"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "481d5dad619343802d0a9adaf9475811"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "10efc2f9b2d626383cf0f72c489318a1"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "207ad9fdcc8d557010ec1bf2ae9f65dc"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "ed22d0517a07f33bb94970063bc605bc"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "71dffb3f63a8dcb09cad4e0b9b8bb69e"});
 
         return tests.toArray(new Object[][]{});
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
index 4434e4464..a4c896e74 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
@@ -28,7 +28,6 @@ package org.broadinstitute.gatk.engine.walkers;
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.index.Index;
 import htsjdk.tribble.index.IndexFactory;
-import htsjdk.tribble.util.TabixUtils;
 import htsjdk.variant.bcf2.BCF2Utils;
 import htsjdk.variant.vcf.VCFCodec;
 import org.apache.commons.lang.StringUtils;